[EMBOSS] Simple configuration of databases - Checked by AntiVir DEM
gbottu at ben.vub.ac.be
Thu Nov 23 19:02:45 UTC 2006
On Thu, Nov 23, 2006 at 09:29:15AM +0300, Maxim Jankov wrote:
> Fortunately, I don't want to download all these gigabytes, and better
> configure emboss to work with all that db's online. But the bad thing is
> that I'm completely stuck in all that manuals and just begging for help of
> someone who done configuration like that and can provide me with ready or
> easy-to-understand config files.
I can provide you just like that with some remote databank definitions we
use at the BEN site. Put in your file .../share/EMBOSS/emboss.default :
DB NCBI_NUC [ type: N method: entrez format: genbank
comment: 'nonredundant nuc. acid db at NCBI (by GI number)'
DB NCBI_PROT [ type: P method: entrez format: genbank
comment: 'nonredundant protein db at NCBI (by GI number)'
DB EBI_EMBL [ type: N methodquery: external format: embl comment: 'EMBL at EBI'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData embl:%s'
DB EBI_EMBLSVA [ type: N methodquery: external format: embl
comment: 'EMBL Sequence Version Archive at EBI (by SV)'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData emblsva:%s'
DB EBI_EMBLCDS [ type: N methodquery: external format: embl
comment: 'EMBL Coding Sequences at EBI (by ProteinID)'
app: '/opt/sw/EBIWS/WSDbfetchClient.pl fetchData emblcds:%s'
Note : EMBOSS does have a databank access method "dbfetch", but I never
managed to get it working (can someone who did tell me how ?). Instead I
use the script WSDbfetchClient.pl (see attachment). To make it work you
will need to install in your Perl the module SOAP-Lite (version 0.60 and
not higher !). You will have to adapt the "app" parameter here above and
the "shebang line" of the script.
Belgian EMBnet Node
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